Resonance Assignment/Abacus/FMCGUI objects: Difference between revisions

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=== Assignment probabilities  ===
=== Assignment probabilities  ===


:&nbsp;&nbsp;&nbsp; FragmentFragment assignment probabilities <span>&nbsp;and &nbsp;are calculated using SA and REM Monte Carlo simulations, respectively. Here ''s'' stands for protein sequence position ID. </span>
:&nbsp;&nbsp;
 
<span>P<sup>s</sup>(f) is a probability of fragment f to be assigned to sequense position s, where f is fragment user ID, and s is sequence position ID.</span>
<br>  
<span>There are two assignment probabilities associated with a fragment - P<sup>s</sup><sub>SA</sub>(f) and P<sup>s</sup><sub>REM</sub>(f) - that are calculated using Simulates Annealing (SA) and  
<div>&nbsp;<span> &nbsp;is calculated&nbsp;by command ['''Assignment&gt;Calculate probabilities&gt;SA'''] or it can be loaded in memory using command ['''Assignment&gt;Load probabilities'''];</span></div><div>&nbsp;<span> &nbsp;is calculated&nbsp;by command ['''Assignment&gt;Calculate probabilities&gt;REM'''] or it can be loaded in memory using command ['''Assignment&gt;Load probabilities'''];</span></div><div>&nbsp;</div><div>The current values of all these properties for a particular fragment could be observed in the “Fragment Graph “window which is opened by command ['''<span>View&gt;Fragment</span>''']</div><div>&nbsp;</div><div>&nbsp;<br></div>
</span>
<span>Replica Exchange Method (REM) Monte Carlo simulations, respistively.</span>
<span><span />
</span> <div>&nbsp;<span>P<sup>s</sup><sub>SA</sub>(f) </span><span>is calculated by command {Assignment&gt;Calculate probabilities&gt;SA} . '''
'''</span></div><div>&nbsp;<span>P<sup>s</sup><sub>REM</sub>(f)&nbsp; </span><span> is calculated&nbsp;by command {Assignment&gt;Calculate probabilities&gt;REM}.</span></div><div><span /></div><div><span>Both assignment probabilities could be also&nbsp; loaded in memory from already performed calculations using command {Assignment&gt;Load probabilities}.</span></div><div>&nbsp;</div><div>The current values of all these properties for a particular fragment could be observed in the “Fragment Graph “window which is opened by command ['''<span>View&gt;Fragment</span>''']</div><div>&nbsp;</div><div>&nbsp;<br></div>


== Main window  ==
== Main window  ==
<div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure 2.1)</div><div>&nbsp;- the title bar displays the name of the current project and the directory where the project is located;</div><div>&nbsp;- the bar with six menu: Project, Data, Fragment, Assignment, Structure, and View, respectively;</div><div>- the main message window, where message from the last executed command is displayed&nbsp;;</div><div>- the log window,&nbsp;where the history of executed commands is shown.</div><div>&nbsp;</div><div>&nbsp;</div>
<div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure 2.1)</div><div>&nbsp;- the title bar displays the name of the current project and the directory where the project is located;</div><div>&nbsp;- the bar with six menu: Project, Data, Fragment, Assignment, Structure, and View, respectively;</div><div>- the main message window, where message from the last executed command is displayed&nbsp;;</div><div>- the log window,&nbsp;where the history of executed commands is shown.</div><div>&nbsp;</div><div>&nbsp;</div>

Revision as of 22:19, 30 November 2009

 

Most of FMCGUI commands operate mainly with the following three objects that are located in computer memory: 
  • protein sequence
  • peak list
  • and PB fragments.
 

Protein sequence

This object can be created in memory using {Data>Protein Sequence>Load } or {Project>Load} commands.
 
 The position ID of the first residue in the sequence should be specified by user upon loading sequence file (in the case it is not specified in the input file). Some commands in FMCGUI implies that the first residue of the protein sequence has position ID of 1. Therefore, if there is HIS-tag, then the loaded sequence should be numbered accordingly starting with a negative position ID of the first residue.
 

Peak list

Different peak lists objects can be created in memory using {Data>”Peak list name”>Load} or {Project>Load}

  • (+)    peak list is required to be referenced
  • (+/-)  peak lists could be referenced optionally 
  • (-)     peak lists for which referencing is not used even if it is present in the input file
                              
N15 NOESY             
-
C13 NOESY H2O     
-
Arom NOESY            
-
N15 HSQC
+
C13 HSQC
+
HNCA
+/-
HNCO
-
CBCACONH
+/-
HBHACONH
+
          
 

 List of PB fragments

This object can be created in memory using {Fragment>Load>}, {Fragment>Create>abacus}, or {Project>Load} commands.
Each PB fragment in the list has the following main properties:

User ID          

     Fragment ID assigned by user, U_id. U_id can’t be changed within FMCGUI.

Assignment ID

    Assignment ID, A_id,  indicates the sequence position ID to which the fragment is assigned.

A_id = -99 if the fragment is not assigned to any position in the sequence.

A_id could be set up or modified by the following commands {Assignment>Fix Assignment>Manually}, {Assignment>Fix Assignment>Using probability Map}, and {Assignment>Fix Assignment>Reset all }.

Typing probabilities

     Tt (f)  is a probability for fragment f to have amino acid type t. Here t corresponds to one of 20 amino acid residue types, and f is fragment user ID.

Typing probbilities  could be calculated or modified manually by the commands {Fragment>Type>Calculate} and  {Fragment>Type>Fix}, respectively.

Contact map

There are three fragment contact maps: Cf1CA(f2)  , Cf1B(f2) ,  and Cf1F(f2) , respectively. Each contact map scores the possibility for any fragment f1 to be next to the fragment f1 in protein sequence. Here f1 and f2 stand for fragment's user ID.
 Fragment contact map  Cf1CA(f2) is calculated based on HNCA spectrum by the command   {Assignment>Contacts>HNCA}
 Fragment   contact maps Cf1B(f2)   and Cf1F(f2) <span />  are calculated from NOESY spectra with or without using BACUS procedure, respectively.
   Cf1F(f2)   can be calculated for all values of f1 and f2 by both commands   {Assignment>Contacts>NOE>fawn}   and {Assignment>Contact>NOE>abacus}, while   Cf1B(f2) <span /> is calculated by  command {Assignment>Contact>NOE>abacus}.
 

Assignment probabilities

  

Ps(f) is a probability of fragment f to be assigned to sequense position s, where f is fragment user ID, and s is sequence position ID. There are two assignment probabilities associated with a fragment - PsSA(f) and PsREM(f) - that are calculated using Simulates Annealing (SA) and Replica Exchange Method (REM) Monte Carlo simulations, respistively.

 PsSA(f) is calculated by command {Assignment>Calculate probabilities>SA} .
 PsREM(f)  is calculated by command {Assignment>Calculate probabilities>REM}.
Both assignment probabilities could be also  loaded in memory from already performed calculations using command {Assignment>Load probabilities}.
 
The current values of all these properties for a particular fragment could be observed in the “Fragment Graph “window which is opened by command [View>Fragment]
 
 

Main window

The main frame of FMC Graphical Interface consist of 4 sections (see Figure 2.1)
 - the title bar displays the name of the current project and the directory where the project is located;
 - the bar with six menu: Project, Data, Fragment, Assignment, Structure, and View, respectively;
- the main message window, where message from the last executed command is displayed ;
- the log window, where the history of executed commands is shown.
 
 
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